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- PDB-9hg2: Crystal structure of M. smegmatis GMP reductase in complex with I... -

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Basic information

Entry
Database: PDB / ID: 9hg2
TitleCrystal structure of M. smegmatis GMP reductase in complex with IMP and ATP.
ComponentsGMP reductase
KeywordsOXIDOREDUCTASE / GMP reductase / GuaB1 / CBS domain / Mycobacterium smegmatis
Function / homology
Function and homology information


GMP reductase / GMP reductase activity / IMP salvage / IMP dehydrogenase activity / purine ribonucleoside salvage / cytosol
Similarity search - Function
GMP reductase-like / : / Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / IMP dehydrogenase / GMP reductase domain / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Aldolase-type TIM barrel
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / INOSINIC ACID / GMP reductase
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsDolezal, M. / Pichova, I.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)LX22NPO5103European Union
CitationJournal: To Be Published
Title: Structural basis for allosteric regulation of mycobacterial guanosine 5'-monophosphate reductase with ATP and GTP.
Authors: Dolezal, M. / Knejzlik, Z. / Kouba, T. / Filimonenko, A. / Svachova, H. / Klima, M. / Pichova, I.
History
DepositionNov 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GMP reductase
B: GMP reductase
C: GMP reductase
D: GMP reductase
E: GMP reductase
F: GMP reductase
G: GMP reductase
H: GMP reductase
I: GMP reductase
J: GMP reductase
K: GMP reductase
L: GMP reductase
M: GMP reductase
N: GMP reductase
O: GMP reductase
P: GMP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)842,20548
Polymers828,51916
Non-polymers13,68632
Water53,5592973
1
A: GMP reductase
B: GMP reductase
C: GMP reductase
D: GMP reductase
E: GMP reductase
F: GMP reductase
G: GMP reductase
H: GMP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)421,10324
Polymers414,2598
Non-polymers6,84316
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area48420 Å2
ΔGint-264 kcal/mol
Surface area124550 Å2
MethodPISA
2
I: GMP reductase
J: GMP reductase
K: GMP reductase
L: GMP reductase
M: GMP reductase
N: GMP reductase
O: GMP reductase
P: GMP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)421,10324
Polymers414,2598
Non-polymers6,84316
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area48270 Å2
ΔGint-264 kcal/mol
Surface area124140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.940, 115.740, 178.920
Angle α, β, γ (deg.)77.748, 83.317, 65.603
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
GMP reductase / Guanosine 5'-monophosphate reductase / GMPR


Mass: 51782.434 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: guaB1, MSMEG_3634, MSMEI_3548 / Plasmid: pTriex / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0QYE8, GMP reductase
#2: Chemical
ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C10H13N4O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2973 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.9
Details: 0.03 M Magnesium chloride 0.03 M Calcium chloride 20% (v/v) Ethylene glycol 10.0% (v/v) PEG 8000 0.1 M Tris/BICINE, pH 8.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 13, 2023
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.6→45.5 Å / Num. obs: 2120483 / % possible obs: 98.64 % / Redundancy: 3.5 % / Biso Wilson estimate: 25.4 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.1209 / Rpim(I) all: 0.0751 / Rrim(I) all: 0.1427 / Net I/σ(I): 6.03
Reflection shellResolution: 1.6→1.62 Å / Redundancy: 3.6 % / Rmerge(I) obs: 4.625 / Mean I/σ(I) obs: 0.28 / Num. unique obs: 70500 / CC1/2: 0.0587 / CC star: 0.333 / Rpim(I) all: 2.806 / Rrim(I) all: 5.421 / % possible all: 93.09

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Processing

Software
NameVersionClassification
XDS20220820data reduction
XSCALE20220820data scaling
PHASER2.8.3phasing
Coot0.9.8.1 ELmodel building
PHENIX1.21_5204refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→45.5 Å / SU ML: 0.2576 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.0282
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2247 52906 5 %
Rwork0.2021 1005594 -
obs0.2032 1058500 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.52 Å2
Refinement stepCycle: LAST / Resolution: 1.6→45.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms53335 0 864 2973 57172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004155894
X-RAY DIFFRACTIONf_angle_d0.649676536
X-RAY DIFFRACTIONf_chiral_restr0.0489117
X-RAY DIFFRACTIONf_plane_restr0.006910114
X-RAY DIFFRACTIONf_dihedral_angle_d13.902220326
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.375316680.368731655X-RAY DIFFRACTION93.09
1.62-1.640.378217200.363932544X-RAY DIFFRACTION95.74
1.64-1.660.37217330.354433059X-RAY DIFFRACTION97.21
1.66-1.680.362417510.346533391X-RAY DIFFRACTION98.15
1.68-1.70.364617580.346533567X-RAY DIFFRACTION98.67
1.7-1.720.352417630.334333567X-RAY DIFFRACTION98.88
1.72-1.750.342617670.323833628X-RAY DIFFRACTION99.05
1.75-1.770.339517750.307933719X-RAY DIFFRACTION99.13
1.77-1.80.307517740.28833686X-RAY DIFFRACTION99.19
1.8-1.830.316517770.282533773X-RAY DIFFRACTION99.24
1.83-1.860.294317730.268133686X-RAY DIFFRACTION99.21
1.86-1.90.288517750.265833722X-RAY DIFFRACTION99.29
1.9-1.930.294917750.25933717X-RAY DIFFRACTION99.26
1.93-1.970.280817740.255633707X-RAY DIFFRACTION99.18
1.97-2.020.271117640.241333517X-RAY DIFFRACTION99
2.02-2.060.263417010.231932306X-RAY DIFFRACTION94.91
2.06-2.110.246417550.215133340X-RAY DIFFRACTION98
2.11-2.170.24417820.208833855X-RAY DIFFRACTION99.64
2.17-2.240.228317820.199133872X-RAY DIFFRACTION99.69
2.24-2.310.233617850.196333917X-RAY DIFFRACTION99.85
2.31-2.390.227617860.192533949X-RAY DIFFRACTION99.9
2.39-2.490.227317900.192933994X-RAY DIFFRACTION99.88
2.49-2.60.230617830.193733879X-RAY DIFFRACTION99.84
2.6-2.740.224417840.199533898X-RAY DIFFRACTION99.83
2.74-2.910.229217880.201833973X-RAY DIFFRACTION99.74
2.91-3.130.2317710.200433636X-RAY DIFFRACTION99.17
3.13-3.450.218117760.195433745X-RAY DIFFRACTION99.23
3.45-3.950.191117130.177232545X-RAY DIFFRACTION95.76
3.95-4.970.155117850.143633919X-RAY DIFFRACTION99.7
4.97-45.50.163517780.155433828X-RAY DIFFRACTION99.66

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